You might zip a PM to
jockbolter50. He's an auto glass installer by profession. He can probably guide you through the process.
Bighouses,firstly welcome.
I'll save you the trouble of typing a message,as Tiny mentions i'm a glass guy but to be honest have little experience with the early 40s Chevy trucks.
Are you referring to the glass/frame rubber or the frame to body seal?
I assume like most windshield frames of that era the frame to body rubber locates in a groove with a 'T' shaped profile?
If so it sounds to me like the extra paint thickness is possibly causing the rubber to bind.
Could you post any pics of the offending part/s to allow a more accurate diagnosis?
Thanks